The CIA and ISI: Are Pakistan and the U.S.’s Spy Agencies Starting to Get Along?

Though the domestic environment in either country is hardly suitable for rapprochement, there are signs of a thaw between the U.S. and Pakistan, particularly in the dealings of their influential spy agencies

After months of relations languishing at an all-time low, Pakistan and the U.S. may now be opening up a fresh phase of engagement. Following U.S. Secretary of State Hillary Clinton’s recent apology for the loss of 24 Pakistani soldiers at a border checkpoint last November, NATO supplies are rumbling through again. Washington has also released funds for Pakistani military operations it had previously withheld. And, perhaps most crucially, the two fractious allies’ top spies are talking again, with a view to enhancing their cooperation as the 2014 deadline for a withdrawal of U.S. troops from Afghanistan looms.

The relationship between the CIA and Pakistan’s Inter-Services Intelligence (ISI) agency has been at the core of Washington and Islamabad’s alliance for over a decade now — and sometimes the source of the mutual misery. After 9/11, both intelligence agencies collaborated closely to capture scores of al-Qaeda suspects. But over the past two years, as suspicions have grown, the two sides have become near adversaries.

The ISI is often accused of supporting jihadist proxies attacking U.S. and NATO troops in Afghanistan — and is widely considered to have been either incompetent or complicit when it came to Osama bin Laden’s presence in Pakistan. The CIA was found to be operating independently within Pakistan’s jealously guarded territory, running unauthorized contractors, recruiting local informants and showering drones at their fiercest pace yet.

But as bitter memories of those disputes begin to recede and new faces assume leadership roles, there is some cautious optimism going forward now — this despite domestic imperatives in both countries (an election year in the U.S., the heated anti-American populism in Pakistan) making rapprochement difficult. Last month the new head of ISI, Lieut. General Zaheer-ul-Islam, made his first visit to Washington, meeting with top intelligence, defense and Administration officials. Tentative agreements were made in terms of joint operations against militants in the region, the Wall Street Journalreported. But, officials from both sides say, fundamental differences linger.

Little is known about General ul-Islam, but a change at the top of ISI will please U.S. security officials. The previous ISI chief, now retired Lieut. General Ahmad Shuja Pasha, had become fiercely hostile to Washington in his final year — engaging in “shouting matches” with then CIA director Leon Panetta, cutting cooperation down to a minimum, ordering the harassment of U.S. diplomats in Pakistan and locking up Shakil Afridi, the physician who ran a vaccination program in the town where bin Laden was found hiding.

Afridi is currently serving a 33-year sentence handed down to him by a tribal court. The charges were not explicitly for spying for the U.S., but there is little doubt in observers’ minds that this is the reason he was punished. Afridi wasn’t arrested for the alleged offenses he has been convicted for until the ISI discovered his vaccination program and links to the CIA. At one point, according to a Pakistani military official familiar with the discussions, the CIA suggested that the ISI strip Afridi of his nationality and hand him over to the U.S. General Pasha angrily refused, saying it would set a bad precedent — one that could encourage others to spy for foreign countries if there were no consequences. U.S. Congressmen reacted angrily to Afridi’s imprisonment, voting to cut $33 million of U.S. assistance to Pakistan, one million for each year he’s serving in prison. The question of Afridi’s fate will likely have come up during ul-Islam’s visit to the U.S. There may be no movement soon, but if relations between Washington and Islamabad grow warmer, the ISI may eventually be persuaded to arrange for Afridi’s quiet release.

The harassment of U.S. officials hasn’t changed much, says a U.S. official. Vehicles are constantly stopped, security personnel searched with unusual rigor, and there is even pressure on the U.S. to abandon the construction of a new consulate in Peshawar. On other fronts, ul-Islam has maintained a low profile, a decision thought to be influenced by his predecessor’s controversial visibility. “Unlike General Pasha,” says a senior politician from Pakistan’s opposition Pakistan Muslim League-Nawaz party, “we don’t see the new head of the ISI interfering in politics — yet.”

During the new ISI chief’s visit, U.S. officials repeated their long-standing concerns about the Haqqani network, a potent jihadist group linked to al-Qaeda that is based in Pakistan’s North Waziristan tribal territory along the Afghan border. From their sanctuary there, say U.S. officials, the group contentedly plots terrorist attacks on U.S. and NATO troops in Afghanistan, before slipping back across the border. The ISI is widely suspected of offering the group support, with Admiral Mike Mullen, former Chairman of the Joint Chiefs of Staff, even describing the Haqqanis as “a veritable arm of the ISI” in his valedictory testimony before Congress last year.

The Pakistanis deny backing the Haqqanis but concede links with them and their reluctance to confront them. They plaintively cite a lack of resources and insist their priority is targeting militants mounting attacks inside Pakistan, but tellingly add that the Haqqanis will be crucial to any future Afghan settlement that Pakistan hopes to be a part of. But a series of unremitting, violent attacks in and around Kabul, authored by the Haqqanis, has intensified the pressure on the Pakistanis.

Last October, Pakistan’s army chief, General Ashfaq Kayani, discussed the possibility of “limiting the space” given to the Haqqanis in North Waziristan with Clinton during her visit to Islamabad. The Pakistani army said it had certain contingency plans in place for limited, surgical operations to reclaim territory in some of North Waziristan’s main towns. These plans were shelved soon after, with the deaths of the Pakistani soldiers in November 2011. Now, as pressure builds again, with enduring attacks and Congressmen calling for the Haqqani network to be designated as a foreign terrorist organization, the plans will have to be revisited. The new U.S. ambassador to Pakistan, Richard Olson, told U.S. lawmakers during his confirmation hearings last month that he will be committed to taking on the Haqqanis.

Without a Pakistani military operation against the Haqqanis, the CIA has focused on drone strikes against them and other militants in the region. The strikes, U.S. officials insist, are effective. Some Pakistani military officials also have conceded improved accuracy. But there are limits to what can be achieved by a drone-only strategy, and there are political costs. Drone strikes have not only become hugely unpopular in Pakistan, where the parliament has united in denouncing them, but also across the world. A Pew Research Center survey published in June found that majorities in countries as diverse as France, Germany, the Czech Republic, China, Japan, Brazil and Turkey opposed the widespread use of drone strikes.

An acknowledgment of the accumulating political costs may temper the frequency with which the CIA uses drone strikes. General David Petraeus, the new CIA director, is said to appreciate that the program is unsustainable. Previous CIA director Panetta was seen as being indulgent of “the CT guys and their shiny toys,” says the official. Drone strikes increased to a pace of one every four days at their height.

But there are certain points at which they are seen as a necessity — and they will continue to be used despite ul-Islam’s insistence last month in Washington that they stop. Just days after Clinton’s apology and the reopening of the NATO supply lines, a drone strike in North Waziristan reportedly killed 20 suspected militants. The actual figure, the U.S. official says, was lower. But it was a truck packed with explosives heading across the border. “It was a clear shot,” the official says. “We had to take it.” And that is one of the many differences in opinion that both sides will somehow have to learn to live with.